This repository includes a way to visualize genom data as scatterplot to find synteny parts.
The project is a perfomance for M-BS2-S4B SS2015 at the Justus-Liebig-University Giessen. For the overview this nice example was used and modified. Brushing is not implemented because d3.brush and d3.zoom both trigger on drag. The links where to look for the genome/gen are hardcoded. The search pattern is individual. The length is calculated from start and end position. This could be a problem when you use circular genomes.
Datafile as JSON. See the example in the files folder. Javascript libraries D3.js and underscore.js.
In the overview click on the plot you want to see in detail. In the single view you can zoom in and out. Also it is possible to mark the dots by clicking and get them into a table. A rightclick on the dots makes it possible to click on the links to the genes and genomes.
The file "data_sets/Arabidopsis/Arabidopsis.Release5.matchList" from DAGchainer: Computing Chains of Syntenic Genes in Complete Genomes was used to fill our own JSON file. Thanks a lot!
You cannot save the marked data/ the table or the SVG itself.
The click to open the single plot only works if not clicked on dots. If drawing a frame (class=frame) only a click on the frame opens a new window.
The MIT License (MIT)
Copyright (c) 2015 Sabine Hurka, Jens Schauer, Mark-Robin Greim
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
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